Synthetic Biology Software

Synthetic biology software we have developed

An important part of our research activity at Virginia Tech was to develop a suite of synthetic biology software applications.

GenoCAD: This is a Computer Assisted Design tool for DNA molecules. Think of it as AutoCAD for DNA. It is a web-based application that includes a module to manage large collections of genetic parts. Another module makes it possible to formalize design rules. The design module itself guides the user through a series of decisions that progressively specify the DNA molecules they are working on. This tool is based on the assumption that synthetic DNA sequences can be represented as computer languages. It includes a grammar editor allowing life scientists with no background in computer science to specify their own domain specific DNA languages for their particular application. This tool was described in several publications:

GenoREAD: This web-based application goal is to make it easier to verify the sequence of their plasmids. The user interface allows users to upload Sanger sequencing traces along with their plasmid reference sequence. The underlying bioinformatics pipeline assembles the traces into a contig and aligns the contig to the reference sequence. Results of the alignment are presented to the user with three flags indicating if the physical sequence matches the reference sequence or not, or it requires manual review. This tool was described in a publication:

GenoSIGHT: This application is used to provide real-time control of a microscope used to observe the dynamics of gene networks in live cells. The application analyzes the images as they are acquired and extracts data allowing the operator to get a sense of the network dynamics. This application is written in MATLAB and was described in one publication: